ROntoTools: R Onto-Tools suite

Suite of tools for functional analysis.

AuthorCalin Voichita <calin@wayne.edu> and Sahar Ansari <saharansari@wayne.edu> and Sorin Draghici <sorin@wayne.edu>
Date of publicationNone
MaintainerCalin Voichita <calin@wayne.edu>
LicenseCC BY-NC-ND 4.0 + file LICENSE
Version2.2.0

View on Bioconductor

Man pages

alpha1MR: Compute alpha weights

alphaMLG: Compute alpha weights

compute.fisher: Combine independent p-values using the Fisher method

compute.normalInv: Combine independent p-values using the normal inversion...

KEGGpathway2Graph: Modified version of the same function from KEGGgraph

keggPathwayGraphs: Download and parse KEGG pathway data

keggPathwayNames: Obtain KEGG pathway titles

nodeWeights: Retrieve the node weights of a graph

pDis: Primary dis-regulation: Pathway analysis approach based on...

pDisPathway-class: Class that encodes the result of pDis analysis for a single...

pDisRes-class: Primary dis-regulation (pDis) result class

pe: Pathway-Express: Pathway analysis of signaling pathways

peEdgeRenderInfo: Extract edge render information from a 'pePathway-class'...

peNodeRenderInfo: Extract node render information from a 'pePathway-class'...

pePathway-class: Class that encodes the result of Pathway-Express for a single...

peRes-class: Pathway-Express result class

plot.pePathway-methods: Plot pathway level statistics

plot.peRes-methods: Plot Pathway-Express result

setEdgeWeights: Set gene weights based on edge type

setNodeWeights: Set node weights

subGraphByNodeType: Modified version of the same function from KEGGgraph

summary.pDisRes: Summarize the results of a primary dis-regulation (pDis)...

Summary-pDisRes-method: Summarize the results of a Pathway-Express analysis

summary.peRes: Summarize the results of a Pathway-Express analysis

Summary-peRes-method: Summarize the results of a Pathway-Express analysis

Files in this package

ROntoTools/DESCRIPTION
ROntoTools/LICENSE
ROntoTools/NAMESPACE
ROntoTools/NEWS
ROntoTools/R
ROntoTools/R/AllClasses.R ROntoTools/R/AllGenerics.R ROntoTools/R/Summary-methods.R ROntoTools/R/graphWeights.R ROntoTools/R/keggDataREST.R ROntoTools/R/nodeWeights-methods.R ROntoTools/R/pDisExpress.R ROntoTools/R/pDisPathway-utils.R ROntoTools/R/pathwayExpress.R ROntoTools/R/pePathway-utils.R ROntoTools/R/plot-methods.R ROntoTools/R/renderInfo-methods.R ROntoTools/R/summary.pDisRes.R ROntoTools/R/summary.peRes.R ROntoTools/R/utils.R
ROntoTools/build
ROntoTools/build/vignette.rds
ROntoTools/inst
ROntoTools/inst/doc
ROntoTools/inst/doc/rontotools.R
ROntoTools/inst/doc/rontotools.Rnw
ROntoTools/inst/doc/rontotools.pdf
ROntoTools/inst/extdata
ROntoTools/inst/extdata/E-GEOD-21942.topTable.RData
ROntoTools/inst/extdata/KEGGRESTunparsed_hsa.RData
ROntoTools/inst/extdata/kpgDefault.RData
ROntoTools/inst/unitTests
ROntoTools/inst/unitTests/test_alpha.R
ROntoTools/inst/unitTests/test_graphWeights.R
ROntoTools/inst/unitTests/test_nodeWeights.R
ROntoTools/inst/unitTests/test_pe.R
ROntoTools/man
ROntoTools/man/KEGGpathway2Graph.Rd ROntoTools/man/Summary-pDisRes-method.Rd ROntoTools/man/Summary-peRes-method.Rd ROntoTools/man/alpha1MR.Rd ROntoTools/man/alphaMLG.Rd ROntoTools/man/compute.fisher.Rd ROntoTools/man/compute.normalInv.Rd ROntoTools/man/keggPathwayGraphs.Rd ROntoTools/man/keggPathwayNames.Rd ROntoTools/man/nodeWeights.Rd ROntoTools/man/pDis.Rd ROntoTools/man/pDisPathway-class.Rd ROntoTools/man/pDisRes-class.Rd ROntoTools/man/pe.Rd ROntoTools/man/peEdgeRenderInfo.Rd ROntoTools/man/peNodeRenderInfo.Rd ROntoTools/man/pePathway-class.Rd ROntoTools/man/peRes-class.Rd ROntoTools/man/plot.pePathway-methods.Rd ROntoTools/man/plot.peRes-methods.Rd ROntoTools/man/setEdgeWeights.Rd ROntoTools/man/setNodeWeights.Rd ROntoTools/man/subGraphByNodeType.Rd ROntoTools/man/summary.pDisRes.Rd ROntoTools/man/summary.peRes.Rd
ROntoTools/tests
ROntoTools/tests/runTests.R
ROntoTools/vignettes
ROntoTools/vignettes/rontotools.Rnw
ROntoTools/vignettes/rontotools.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.